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From what I understand, when energy is supplied to quarks, it elongates the gluon tube and when enough energy is put in, new quarks are formed, keeping quark confinement. However, I am inquisitive from an experimental point of view about how this is performed to give us the information we know. More specifically, how do scientists supply energy to the quarks?

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As the comments say: smash. One way to do this is called deep inelastic scattering (DIS):

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This was originally done at SLAC with an electron beam on liquid hydrogen and deuterium targets. Since the beam and scattered electron momenta are known, the energy and momentum (and longitudinal polarization) of the exchanged tree-level photons is known. This led to the confirmation of 3 valence quarks with charges of $+\frac 2 3$ and $-\frac 1 3$, and sea-quarks, and gluons (see: 3-jet events). It also showed that quarks only carry half of the nucleon momentum.

If you just detect the electron, it's called inclusive DIS. With coincidence detection of one or more (but not all) of the hadronic products, it's semi-inclusive DIS, which allows tagging the struck quark (which "get dressed" on its way out). TJNAF was designed to do this.

With polarized electron beams and targets the spin / angular momentum state inside the nucleon (or nucleus) can be studied, as the virtual photon can be circularly polarized. From these experiments, it appears the proton spin is not just the $S = \frac 1 2$ state of 3 quarks. (See: Proton Spin Crisis).

It's also done with muon beams, and neutrino beams.

From all the data (which is a lot), so-called Parton-distributions functions are tabulated and are essential to understanding the signal and background processes in $pp$ colliders such as LHC.

Regarding the hadronization process, it was studied at Fermilab (E665), searching for a process called Color Transparency. Here the struck quark takes some time to evolve into a hadron, and should thus be able to pass through nuclear matter more easily. The experiment involved measuring deep inelastic scattering of various nuclear targets and looking for a dependency on the nuclear size ($A$). There was also an experiment at SLAC (NE18), which look at elastic $A(e, e'p)$ scattering, with the idea that at wavelengths much smaller than a proton size, the struck proton is in a small state, and would traverse the nuclear matter before evolving into a normal proton.

I was an author on one of those experiments, and can't remember much more than that. See: https://arxiv.org/pdf/hep-ph/9311238.pdf .

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